CONTENTS

1. Downloading Summary

2. Carbon Use Efficiency

2a. Unconstrained CUE

Phylogenetic Analysis

2b. Constrained CUE

Uptake Kinetics

Effect Sizes

1

Downloading Summary

The DOE knowledgebase (kBASE) was searched for genomes from six major phyla found in soil microbial communities. A total of 24,268 genomes were found to correspond to the six major phyla. Results were trimmed to eliminate duplicates within a given genus, resulting in 1,082 unique genera. These genera were searched in the primary literature to determine habitat preference, and eliminate non-soil bacterial species. Ultimately, 231 species were selected for analysis.

Genomes Genera Selections
Alpha 1709 197 32
Beta 1092 114 30
Gamma 7731 240 19
Delta 185 56 10
Actino 4055 191 25
Acido 25 12 25
Firm 8668 233 25
Verr 36 9 36
Plancto 29 12 29

Note: most of the subsequent analyses currently include only Actino, Acido, Verr, Plancto and Betaproteobacteria.

## null device 
##           1

A database of exchange reactions was built to represent the full range of metabolites possible for uptake across all models. Number of C atoms and Gibbs free energy were noted for each metabolite. Models were compared for similarity of exchange reaction identity using MDS ordination.

## Run 0 stress 0.193728 
## Run 1 stress 0.1916959 
## ... New best solution
## ... procrustes: rmse 0.01880379  max resid 0.1134417 
## Run 2 stress 0.1930628 
## Run 3 stress 0.2056006 
## Run 4 stress 0.4148659 
## Run 5 stress 0.2061946 
## Run 6 stress 0.2167616 
## Run 7 stress 0.1980802 
## Run 8 stress 0.200008 
## Run 9 stress 0.1963522 
## Run 10 stress 0.1937525 
## Run 11 stress 0.2312129 
## Run 12 stress 0.1937272 
## Run 13 stress 0.2125163 
## Run 14 stress 0.1944729 
## Run 15 stress 0.202756 
## Run 16 stress 0.2215017 
## Run 17 stress 0.2230842 
## Run 18 stress 0.1951894 
## Run 19 stress 0.2014534 
## Run 20 stress 0.2007262

2

CARBON USE EFFICIENCY

CUE=(Net C Uptake - Respiration)/(Total C Uptake)

Carbon use efficiency was explored under two scenarios. (1) Unconstrained CUE was calculated by allowing a model to utilize all exchange reactions present, and (2) Constrained CUE was calculated by limiting the availability of a single constraining C-containing metabolite while leaving all other unconstrained.

2a

UNCONSTRAINED CUE

Unconstrained CUE ranged from 0.077259 to 0.916791. Average unconstained CUE was 0.5338781 +/- 0.1642163.

2a1

Phylogenetic Analyses

Unconstrained CUE was analyzed for a phylogenetic signal. K values of 1 correspond to a Brownian motion process, which implies some degree of phylogenetic signal or conservatism. K values closer to zero correspond to a random or convergent pattern of evolution, while K values greater than 1 indicate strong phylogenetic signal and conservatism of traits.

Unconstrained CUE was found to have a significant phylogenetic signal (K = 0.03, p<0.01).

The following heat maps show trait distribution across the phylogenetic tree. Exrxns = number of exchange reactions, Cexrxns = number of C-containing exchange reactions, CUE=unconstrained carbon use efficiency, GC=guanine-cytosine, Genes= number of genes, DNA size= number of base pairs.

K PIC.variance.obs PIC.variance.rnd.mean PIC.variance.P PIC.variance.Z
Exrxns 0.1640496 2.051194e+03 3.681776e+04 0.001 -2.5807560
Cexrxns 0.1725261 1.635154e+03 3.092815e+04 0.001 -2.6985569
CUE 0.0377776 9.143651e-01 3.866792e+00 0.003 -1.8840388
GC 1.2898714 7.349652e+01 1.006113e+04 0.001 -2.7610550
Contigs 0.1758305 4.540426e+06 1.011696e+08 0.008 -0.7268392
Genes 0.3146108 1.591306e+07 5.702364e+08 0.001 -2.5990916
DNAsize 0.5020087 1.307122e+13 7.391281e+14 0.001 -2.6955093

Phylogenetic Independent Contrasts were used to test for relationships between CUE and genome traits.

Intercept Slope R-Adj
Exrxns 0.9608944 -0.0039505 0.1457687
Cexrxns 0.8801619 -0.0042273 0.1393639
GC 0.9156732 -0.0063604 0.0995834
Genes 0.7608438 -0.0000448 0.2943128
DNAsize 0.7659457 0.0000000 0.3229883

2b

CONSTRAINED CUE

For each model in the unconstrained environment, C-containing exchange reactions were classified according to the following hierarchy:

  1. Utilized: reactions utilized by the model in the unconstrained environment.
  1. Essential: reactions that are required for biomass production, identified as reactions that result in no biomass production when availability is set to zero.
  1. Constraining: reactions that biomass production responds to the availability of, i.e. reactions needed at more than a low threshold.

The uptake kinetics of the most common constraining reactions across models were analyzed. The availability of constraining reactions was then set to the concentration resulting in (a) 1/2 and (b) 1/4 of maximum biomass and CUE was recalculated.

2b1

Uptake Kinetics

The uptake kinetics were compared for the most common constraining C-containing exchange reactions. Preliminarily, it appears that uptake kinetics for a given metabolite do not vary between models, but that different metabolite have different uptake kinetics. Biomass flux v. substrate-specific uptake was plotted for a single acidobacterial model and curves were fit with linear model and Michaelis-Menten (MM) models. Both fits were assessed at 50% max biomass and 25% max biomass, and the substrate concentrations at these values from the LM fits were used as uptake bounds for the constrained CUE calculations.

gly.phe.10K = the upper bound of all reactions was increased by one or order of magnitude. gly.phe.10K1K = upper bound of all intracellular reactions and biomass production set to one order of magnitude greater than exchange reactions.

Fitting LM and MM Models to Uptake Kinetics

uptake L.Lysine Gly.Phe.1K Gly.Phe.10K Gly.Phe.10K1K ocdca TRHL Gly.Tyr ddca gly.asn.L L.Isoleucine Myristic.acid Ala.His L.Phenylalanine L.Arginine L.Tyrosine D.Arabinose Cytidine L.Valine L.Proline L.Histidine Glycerol.3.phosphate
Km NA 155.1838328 50.4380138 6.378709e+02 514.564269 30.9441102 58.63531 28.0279135 58.63531 103.470412 125.531434 75.7168209 27.6516428 78.5264815 99.88237 55.45183 25.5975707 128.4957229 173.4981942 102.244632 27.6516428 99.045680
Vm NA 1097.0794735 1053.1013772 1.136925e+04 9876.940300 1047.5678450 1056.66670 1046.9682062 1056.66670 1079.640287 1087.261558 1065.2770580 1046.8203125 1066.7497918 1077.89557 1055.20884 1046.0672293 1088.3203816 1100.9812684 1078.429742 1046.8203125 1077.465721
lm-intercept NA -0.0000267 0.0000045 1.444028e-01 12.425781 -0.0000044 0.00000 0.0000044 0.00000 0.000014 -0.000027 -0.0000045 -0.0000167 0.0000091 0.00000 0.00000 -0.0000167 0.0000054 -0.0000076 9.087836 -0.0000167 0.000000
lm-slope NA 3.2211451 8.7803970 8.779215e+00 8.695916 11.7392473 7.99661 12.4926327 7.99661 4.979316 4.135675 6.6638419 12.6161319 6.4716755 5.17069 8.28661 13.3276840 4.0328230 2.8390284 4.875667 12.6161319 5.217443
uptake at 500 NA 155.2243107 56.9450328 5.693625e+01 56.069331 42.5921688 62.52650 40.0235890 62.52650 100.415406 120.899252 75.0317927 39.6318000 77.2597443 96.69889 60.33830 37.5158966 123.9826288 176.1165937 100.686157 39.6318000 95.832379
uptake at 250 NA 77.6121595 28.4725162 2.845990e+01 27.320205 21.2960846 31.26325 20.0117943 31.26325 50.207701 60.449629 37.5158967 19.8159007 38.6298715 48.34945 30.16915 18.7579489 61.9913137 88.0582982 49.411121 19.8159007 47.916189

2b2

Constraint Effect Size

Constrained CUE was reduced relative to unconstrained CUE, but the effect size varied by metabolite. Plots show unconstrained CUE versus constrained CUE for most common constraining metabolite at 50% maximum biomass and at 25% maximum biomass.

CONSTRAINED/UNCONSTRAINED COMPARISONS AND COHENS D

Cohens D Paired T-test Pval
his500 0.187 0.228
cyt500 0.393 0.007
pro500 0.104 0.331
arg500 0.298 0.001
phenyl500 0.324 0.033
myristic500 0.302 0.001
isoleucine500 0.412 0.000
tyr500 0.461 0.005
glyasn500 0.505 0.000
alahis500 0.458 0.000
ddca500 0.593 0.000
trhl500 0.710 0.000
g3p500 0.000 1.000
ocdca500 0.793 0.000
ara500 0.855 0.000
glytyr500 0.809 0.000
lys500 1.576 0.000
glyphe500 1.330 0.000
val250 0.164 0.117
his250 0.211 0.174
cyt250 0.534 0.000
pro250 0.068 0.528
arg250 0.335 0.000
phenyl250 0.509 0.001
myristic250 0.267 0.003
isoleucine250 0.442 0.000
tyr250 0.429 0.009
glyasn250 0.536 0.000
alahis250 0.526 0.000
ddca250 0.672 0.000
trhl250 0.894 0.000
g3p250 0.000 0.997
ocdca250 0.886 0.000
ara250 1.176 0.000
glytyr250 0.891 0.000
lys250 1.875 0.000
glyphe250 1.408 0.000